Limosilactobacillus fermentum in the theoretical composition was changed to Lactobacillus fermentum
## Error in validObject(.Object) : invalid class "otu_table" object:
## OTU abundance data must have non-zero dimensions.
## Error in dimnames(x) <- dn :
## length of 'dimnames' [1] not equal to array extent
These are the taxa that were found in the experimental data
## species taxid superkingdom phylum
## 1 Bacillus subtilis 1423 Bacteria Firmicutes
## 2 Enterococcus faecalis 1351 Bacteria Firmicutes
## 3 Escherichia coli 562 Bacteria Proteobacteria
## 4 Limosilactobacillus fermentum 1613 Bacteria Firmicutes
## 5 Listeria monocytogenes 1639 Bacteria Firmicutes
## 6 Pseudomonas aeruginosa 287 Bacteria Proteobacteria
## 7 Salmonella enterica 28901 Bacteria Proteobacteria
## 8 Staphylococcus aureus 1280 Bacteria Firmicutes
## class order family genus
## 1 Bacilli Bacillales Bacillaceae Bacillus
## 2 Bacilli Lactobacillales Enterococcaceae Enterococcus
## 3 Gammaproteobacteria Enterobacterales Enterobacteriaceae Escherichia
## 4 Bacilli Lactobacillales Lactobacillaceae Limosilactobacillus
## 5 Bacilli Bacillales Listeriaceae Listeria
## 6 Gammaproteobacteria Pseudomonadales Pseudomonadaceae Pseudomonas
## 7 Gammaproteobacteria Enterobacterales Enterobacteriaceae Salmonella
## 8 Bacilli Bacillales Staphylococcaceae Staphylococcus
## count Gram Stain EXP_sum
## 1 1740000 + NA
## 2 990000 + 73.20904
## 3 1010000 - 6077.60892
## 4 1840000 + NA
## 5 1410000 + NA
## 6 420000 - NA
## 7 1040000 - NA
## 8 1550000 + NA
## Square root transformation
## Wisconsin double standardization
## Run 0 stress 0.1470839
## Run 1 stress 0.1646013
## Run 2 stress 0.1718542
## Run 3 stress 0.1825241
## Run 4 stress 0.1601833
## Run 5 stress 0.1721381
## Run 6 stress 0.1722551
## Run 7 stress 0.1841597
## Run 8 stress 0.1590276
## Run 9 stress 0.1616144
## Run 10 stress 0.181801
## Run 11 stress 0.1674317
## Run 12 stress 0.1669914
## Run 13 stress 0.1750451
## Run 14 stress 0.1505306
## Run 15 stress 0.1615029
## Run 16 stress 0.1744525
## Run 17 stress 0.1736455
## Run 18 stress 0.1548971
## Run 19 stress 0.1766343
## Run 20 stress 0.1763632
## *** Best solution was not repeated -- monoMDS stopping criteria:
## 20: stress ratio > sratmax
## taxon p_value significant label
## <char> <num> <lgcl> <char>
## 1: Actinobacteria 1.117457e-01 FALSE
## 2: Bacteroidetes 1.744864e-07 TRUE *
## 3: Cyanobacteria 3.234749e-01 FALSE
## 4: Deferribacteres 2.941912e-01 FALSE
## 5: Firmicutes 8.161593e-10 TRUE *
## 6: Fusobacteria 2.203607e-07 TRUE *
## 7: Proteobacteria 8.974304e-05 TRUE *
## 8: Synergistetes 3.234749e-01 FALSE
## 9: Tenericutes 1.157477e-01 FALSE
Full-model PERMANOVA: source + dna.isolation.method
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Blocks: strata
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = otutab_t ~ sex + dna.isolation.methods + date, data = sampdat, method = distance, by = "terms", strata = sampdat$source)
## Df SumOfSqs R2 F Pr(>F)
## sex 1 0.0586 0.00962 1.0000 0.001 ***
## dna.isolation.methods 1 1.1305 0.18547 19.2805 0.001 ***
## date 13 1.1537 0.18927 1.5135 0.051 .
## Residual 64 3.7526 0.61564
## Total 79 6.0954 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## taxon p_value significant label
## <char> <num> <lgcl> <char>
## 1: Acidaminococcales 6.797769e-06 TRUE *
## 2: Aeromonadales 3.016794e-03 TRUE *
## 3: Anaeroplasmatales 1.157477e-01 FALSE
## 4: Bacillales 2.029339e-01 FALSE
## 5: Bacteroidales 1.746399e-07 TRUE *
## 6: Bifidobacteriales 1.673634e-01 FALSE
## 7: Burkholderiales 1.135086e-05 TRUE *
## 8: Campylobacterales 5.593058e-04 TRUE *
## 9: Chroococcidiopsidales 3.234749e-01 FALSE
## 10: Clostridiales 1.765966e-13 TRUE *
## 11: Coriobacteriales 4.849193e-02 TRUE *
## 12: Deferribacterales 2.941912e-01 FALSE
## 13: Eggerthellales 3.811809e-01 FALSE
## 14: Enterobacterales 9.308357e-02 FALSE
## 15: Erysipelotrichales 1.672772e-01 FALSE
## 16: Fusobacteriales 2.203607e-07 TRUE *
## 17: Lactobacillales 9.958588e-03 TRUE *
## 18: Micrococcales 1.914214e-01 FALSE
## 19: Nostocales 3.234749e-01 FALSE
## 20: Oscillatoriales 3.234749e-01 FALSE
## 21: Pleurocapsales 3.234749e-01 FALSE
## 22: Pseudomonadales 2.368003e-01 FALSE
## 23: Selenomonadales 3.791984e-07 TRUE *
## 24: Synechococcales 3.234749e-01 FALSE
## 25: Tissierellales 3.234749e-01 FALSE
## taxon p_value significant label
Full-model PERMANOVA: source + dna.isolation.method
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Blocks: strata
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = otutab_t ~ sex + dna.isolation.methods + date, data = sampdat, method = distance, by = "terms", strata = sampdat$source)
## Df SumOfSqs R2 F Pr(>F)
## sex 1 0.2456 0.02440 2.8907 0.001 ***
## dna.isolation.methods 1 1.9654 0.19524 23.1302 0.001 ***
## date 13 2.4172 0.24012 2.1882 0.001 ***
## Residual 64 5.4383 0.54023
## Total 79 10.0666 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## taxon p_value significant label
## <char> <num> <lgcl> <char>
## 1: Acidaminococcales 6.797769e-06 TRUE *
## 2: Aeromonadales 3.016794e-03 TRUE *
## 3: Anaeroplasmatales 1.157477e-01 FALSE
## 4: Bacillales 2.029339e-01 FALSE
## 5: Bacteroidales 1.746399e-07 TRUE *
## 6: Bifidobacteriales 1.673634e-01 FALSE
## 7: Burkholderiales 1.135086e-05 TRUE *
## 8: Campylobacterales 5.593058e-04 TRUE *
## 9: Chroococcidiopsidales 3.234749e-01 FALSE
## 10: Clostridiales 1.765966e-13 TRUE *
## 11: Coriobacteriales 4.849193e-02 TRUE *
## 12: Deferribacterales 2.941912e-01 FALSE
## 13: Eggerthellales 3.811809e-01 FALSE
## 14: Enterobacterales 9.308357e-02 FALSE
## 15: Erysipelotrichales 1.672772e-01 FALSE
## 16: Fusobacteriales 2.203607e-07 TRUE *
## 17: Lactobacillales 9.958588e-03 TRUE *
## 18: Micrococcales 1.914214e-01 FALSE
## 19: Nostocales 3.234749e-01 FALSE
## 20: Oscillatoriales 3.234749e-01 FALSE
## 21: Pleurocapsales 3.234749e-01 FALSE
## 22: Pseudomonadales 2.368003e-01 FALSE
## 23: Selenomonadales 3.791984e-07 TRUE *
## 24: Synechococcales 3.234749e-01 FALSE
## 25: Tissierellales 3.234749e-01 FALSE
## taxon p_value significant label
Full-model PERMANOVA: source + dna.isolation.method
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Blocks: strata
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = otutab_t ~ sex + dna.isolation.methods + date, data = sampdat, method = distance, by = "terms", strata = sampdat$source)
## Df SumOfSqs R2 F Pr(>F)
## sex 1 0.3503 0.02341 2.8762 0.001 ***
## dna.isolation.methods 1 3.2119 0.21461 26.3718 0.001 ***
## date 13 3.6093 0.24116 2.2796 0.001 ***
## Residual 64 7.7948 0.52082
## Total 79 14.9663 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## taxon p_value significant label
## <char> <num> <lgcl> <char>
## 1: Anaerobiospirillum succiniciproducens 4.820577e-03 TRUE *
## 2: Blautia glucerasea 1.705144e-11 TRUE *
## 3: Blautia hansenii 3.010974e-01 FALSE
## 4: Blautia producta 1.055413e-08 TRUE *
## 5: Blautia sp. N6H1-15 1.220307e-04 TRUE *
## 6: Clostridium perfringens 5.166682e-01 FALSE
## 7: Enterocloster bolteae 1.313457e-09 TRUE *
## 8: Faecalibacterium prausnitzii 7.687366e-06 TRUE *
## 9: Faecalimonas umbilicata 1.039283e-07 TRUE *
## 10: Fusobacterium perfoetens 3.881664e-07 TRUE *
## 11: Fusobacterium varium 2.208536e-06 TRUE *
## 12: Lactobacillus animalis 1.562315e-02 TRUE *
## 13: Lactobacillus johnsonii 5.637611e-01 FALSE
## 14: Lactobacillus reuteri 1.498909e-01 FALSE
## 15: Megamonas funiformis 7.241348e-05 TRUE *
## 16: Megamonas hypermegale 2.581652e-08 TRUE *
## 17: Megamonas rupellensis 7.436912e-07 TRUE *
## 18: Peptacetobacter hiranonis 6.127696e-13 TRUE *
## 19: Phascolarctobacterium succinatutens 6.797769e-06 TRUE *
## 20: Phocaeicola plebeius 1.918687e-07 TRUE *
## 21: Romboutsia timonensis 7.379722e-01 FALSE
## 22: Streptococcus equinus 6.336182e-02 FALSE
## 23: Streptococcus lutetiensis 4.101400e-02 TRUE *
## 24: Turicibacter sp. H121 1.922370e-01 FALSE
## 25: [Ruminococcus] gnavus 9.990586e-01 FALSE
## taxon p_value significant label
Full-model PERMANOVA: source + dna.isolation.method
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Blocks: strata
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = otutab_t ~ sex + dna.isolation.methods + date, data = sampdat, method = distance, by = "terms", strata = sampdat$source)
## Df SumOfSqs R2 F Pr(>F)
## sex 1 0.3730 0.02338 2.7969 0.001 ***
## dna.isolation.methods 1 3.2992 0.20679 24.7391 0.001 ***
## date 13 3.7468 0.23485 2.1612 0.001 ***
## Residual 64 8.5350 0.53498
## Total 79 15.9539 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1